Maps

library(tidy)
library(sf)
library(rnaturalearth)

read_csv("matmort_countries_long.csv")
world_sf <- ne_countries(scale = "medium", returnclass = "sf")

# Identify matches and approximate string matches between matmort and world_map region names:
matmort_regions <- unique(matmort_countries_long$country)
world_sf_regions <- unique(world_sf$name)

country_distances <- 
  # Quantify all pairwise string similarity between matmort_regions and world_map_regions:
  stringdist::stringdistmatrix(matmort_regions, world_sf_regions) %>%
  as.data.frame() %>%
  rownames_to_column(var = "worldbank_country") %>%
  pivot_longer(cols = -worldbank_country, 
               names_to = "world_sf_country", 
               values_to = "Dist") %>%
  # drop V from world_sf_country using stringr package:
  mutate(world_sf_country = str_remove(world_sf_country, "V")) %>%
  # insert country names:
  mutate(worldbank_country = matmort_regions[as.integer(worldbank_country)],
         world_sf_country = world_sf_regions[as.integer(world_sf_country)])

# Countries without an exact match
unmatched_worldbank_countries <- 
  country_distances %>% 
  group_by(worldbank_country) %>%
  mutate(exact_match = min(Dist) == 0) %>%
  ungroup() %>%
  filter(!exact_match) %>%
  distinct(worldbank_country) %>%
  arrange(worldbank_country) %>%
  pull()

unmatched_world_sf_countries <- 
  country_distances %>% 
  group_by(world_sf_country) %>%
  mutate(exact_match = min(Dist) == 0) %>%
  ungroup() %>%
  filter(!exact_match) %>%
  distinct(world_sf_country) %>%
  arrange(world_sf_country) %>%
  pull()

matmort_countries_long <- 
  matmort_countries_long %>%
  mutate(country = 
           # Match countries in 'unmatched_worldbank_countries'
           # by hand, using 'unmatched_world_sf_countries'
           case_when(
             country == "Antigua and Barbuda" ~ "Antigua and Barb.",
             country == "Bahamas, The" ~ "Bahamas",
             country == "Bosnia and Herzegovina" ~ "Bosnia and Herz.",
             country == "British Virgin Islands" ~ "British Virgin Is.",
             country == "Brunei Darussalam" ~ "Brunei",
             country == "Cayman Islands" ~ "Cayman Is.",
             country == "Central African Republic" ~ "Central African Rep.",
             country == "Channel Islands" ~ "Channel Is.",
             country == "Congo, Dem. Rep." ~ "Dem. Rep. Congo",
             country == "Congo, Rep." ~ "Congo",
             country == "Dominican Republic" ~ "Dominican Rep.",
             country == "Egypt, Arab Rep." ~ "Egypt",
             country == "Equatorial Guinea" ~ "Eq. Guinea",
             country == "Eswatini" ~ "eSwatini",
             country == "Faroe Islands" ~ "Faeroe Is.",
             country == "French Polynesia" ~ "Fr. Polynesia",
             country == "Gambia, The" ~ "Gambia",
             country == "Hong Kong SAR, China" ~ "Hong Kong",
             country == "Iran, Islamic Rep." ~ "Iran",
             country == "Korea, Dem. People's Rep." ~ "North Korea",
             country == "Korea, Rep." ~ "South Korea",
             country == "Kyrgyz Republic" ~ "Kyrgyzstan",
             country == "Lao PDR" ~ "Laos",
             country == "Macao SAR, China" ~ "Macao",
             country == "Marshall Islands" ~ "Marshall Is.",
             country == "Micronesia, Fed. Sts." ~ "Micronesia",
             country == "Northern Mariana Islands" ~ "N. Mariana Is.",
             country == "Russian Federation" ~ "Russia",
             country == "Sint Maarten (Dutch part)" ~ "Sint Maarten",
             country == "Slovak Republic" ~ "Slovakia",
             country == "Solomon Islands" ~ "Solomon Is.",
             country == "South Sudan" ~ "S. Sudan",
             country == "St. Lucia" ~ "Saint Lucia",
             country == "St. Martin (French part)" ~ "St-Martin",
             country == "St. Vincent and the Grenadines" ~ "St. Vin. and Gren.",
             country == "Syrian Arab Republic" ~ "Syria",
             country == "Turks and Caicos Islands" ~ "Turks and Caicos Is.",
             country == "Türkiye" ~ "Turkey",
             country == "United States" ~ "United States of America",
             country == "Venezuela, RB" ~ "Venezuela",
             country == "Viet Nam" ~ "Vietnam",
             country == "Virgin Islands (U.S.)" ~ "U.S. Virgin Is.",
             country == "West Bank and Gaza" ~ "West Bank",
             country == "Yemen, Rep." ~ "Yemen",
             # these are all the matched countries
             TRUE ~ country
           )) 

# Join matmort data with the world map
matmort_sf <- 
  full_join(world_sf, matmort_countries_long, by = c("name" = "country"))


# Plot using geom_sf 
# choose which projection you want by uncommenting out the appropriate
# st_transform() line
matmort_sf %>%
  # Keep only 2000 (countries with is.na(year) have no data on maternal mortality
  # and are therefore also kept
  filter(year %in% c(2000) | is.na(year)) %>% 
  # Geographic Coordinate System:
  # st_transform(4326) %>% 
  # world equal area:
  # st_transform(8857) %>% 
  # world mercator:
  # st_transform(3857) %>% 
  # Azimuthal Equidistant:
  st_transform(crs = "+proj=aeqd +datum=WGS84 +lon_0=0 +lat_0=0 +x_0=0 +y_0=0 +units=m +no_defs") %>%
  ggplot() +
  geom_sf(aes(fill = log10(incidence))) +
  scale_fill_gradient(name = expression(log[10]~incidence),low = "white", high = "red", na.value = "grey50")# +
  # Use this for the world mercator otherwise Antarctica looks even more ridiculous:
  #coord_sf(ylim = c(-1.3e7, 1.8e7))